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Biology subjects

Konki, M.

Publications and source records attributed to Konki, M..

3 recordsLinked to original sources

From maternal glucocorticoid and thyroid hormones to epigenetic regulation of gene expression: an experimental study in a wild bird species

Offspring phenotype at birth is determined by its genotype and the prenatal environment including exposure to maternal hormones. Variation in both maternal glucocorticoids and thyroid hormones can affect offspring phenotype. However, the underlying molecular mechanisms shaping the offspring phenotype, especially those contributing to long-lasting effects, remain unclear. Epigenetic changes (such as DNA methylation) have been postulated as mediators of long-lasting effects of early-life environment. In this study, we determined the effects of elevated prenatal glucocorticoid and thyroid hormones on handling stress response (breath rate), DNA methylation and gene expression of glucocorticoid receptor (GCR) and thyroid hormone receptor (THR) in great tit (Parus major). Eggs were injected before incubation onset with corticosterone (main avian glucocorticoid) and/or thyroid hormones (thyroxine and triiodothyronine) to simulate variation in maternal hormone deposition. Breath rate during handling and gene expression of GCR and THR were evaluated 14 days after hatching. Methylation status of GCR and THR genes were analyzed from the longitudinal blood samples taken 7 and 14 days after hatching, as well as in the following autumn. Elevated prenatal corticosterone level significantly increased the breath rate during handling, indicating enhanced stress response and/or metabolism. Prenatal corticosterone manipulation had CpG-site-specific effects on DNA methylation at the GCR putative promoter region, while it did not significantly affect GCR gene expression. GCR expression was negatively associated with earlier hatching date and chick size. THR methylation or expression did not exhibit any significant relationship with the hormonal treatments or the examined covariates, suggesting that TH signaling may be more robust due to its crucial role in development. This study supports the view that maternal corticosterone may influence offspring metabolism and stress response via epigenetic alterations, yet their possible adaptive role in optimizing offspring phenotype to the prevailing conditions, context-dependency, and the underlying molecular interplay needs further research.

evolutionary biology↗

Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease

Alzheimers disease (AD) results from a neurodegenerative process that starts well before the diagnosis can be made. New prognostic or diagnostic markers enabling early intervention into the disease process would be highly valuable. As life style factors largely modulate the disease risk, we hypothesised that the disease associated DNA methylation signatures are detectable in the peripheral blood of discordant twin pairs. Reduced Representation Bisulfite Sequencing, single cell RNA-sequencing and gene array data were utilised to examine DNA methylation signatures and associated gene expression changes in blood and hippocampus, and targeted bisulfite sequencing in cross cohort validation. Our results reveal that discordant twin pairs have disease associated differences in their peripheral blood epigenomes. A subset of affected genes, e.g. ADARB2 contain differentially methylated sites also in anterior hippocampus. The DNA methylation differences seem to influence gene expression in brain rather than in blood cells. The affected genes are associated with neuronal functions and pathologies. These DNA methylation signatures are valuable disease marker candidates and may provide insights into the molecular mechanisms of pathogenesis.

genomics↗

LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis

DNA methylation is measured using bisulfite sequencing (BS-seq). Bisulfite conversion can have low efficiency and a DNA sample is then processed multiple times generating DNA libraries with different bisulfite conversion rates. Libraries with low conversion rates are excluded from analysis resulting in reduced coverage and increased costs. We present a method and software, LuxRep, that accounts for technical replicates from different bisulfite-converted DNA libraries. We show that including replicates with low bisulfite conversion rates generates more accurate estimates of methylation levels and differentially methylated sites.\n\nAvailabilityAn implementation of the method is available at https://github.com/tare/LuxGLM/tree/master/LuxRep\n\nContactmaia.malonzo@aalto.fi

bioinformatics↗